Photosensitivity gene of plant and utilization thereof

ABSTRACT

The present inventors successfully isolated a photoperiod sensitivity gene Hd6 from rice by a linkage analysis. It was revealed that the photoperiod sensitivity of plants can be modified by introducing the gene or controlling the expression of the gene. Further, it was demonstrated that the photoperiod sensitivity of plants can be assessed by detecting the presence or absence of the functional gene.

TECHNICAL FIELD

The present invention relates to genes involved in plant photoperiod sensitivity, and methods for modifying photoperiod sensitivity in plants using the genes. Methods to modify plant photoperiod sensitivity are useful for breeding plants.

BACKGROUND ART

Generally, heading (flowering) of rice is accelerated by short-day and delayed by long-day conditions. Among known cultivars, typically those from Kyushu and the south of Mainland Japan have strong photoperiod sensitivity whereas cultivars from the Tohoku district or Hokkaido show complete loss of such sensitivity or have extremely weak photoperiod sensitivity. Rice plants that lack the photoperiod sensitivity have a characteristic to flower after a certain length of growth period, and the heading date of the plant does not change with changes of photoperiod. Adaptation of rice plants related to cultivation locations and season drastically changes in accordance with the existence of photoperiod sensitivity in the plant. Thus, modification of photoperiod sensitivity in rice is an important aspect of breeding rice.

In conventional breeding programs, the alteration of the heading date of rice is achieved through methods involving: (1) selection of early maturing varieties or late varieties by crossing; and (2) mutagenesis by radiation and chemicals; and so on. However, such breeding programs require long periods of time to be successful, and bear other problems, such as unpredictability of the degree or direction of the mutations in the progeny.

“Photoperiod sensitivity gene” is a generic name for genes that enhance the rice photoperiod sensitivity in the field of rice genetics. The existence of several photoperiod sensitivity genes has been observed to be inherent in mutants and cultivars, and photoperiod sensitivity genes are suggested to exist on loci, for example, such as Se1 locus (chromosome 6; Yokoo and Fujimaki (1971) Japan. J. Breed. 21: 35–39), E1 locus (chromosome 7; Tsai, K. H. (1976) Jpn. J. Genet. 51: 115–128; Okumoto, Y. et al. (1992) Jpn. J. Breed. 42: 415–429), E2 locus (unknown), E3 locus (chromosome 3?; Okumoto et al. Japanese Society of Breeding, 91st lecture, Japanese Journal of Breeding 47 (Suppl. 1): 31); and so on (Yamagata et al. (1986) In Rice Genetics, International Rice Research Institute, Manilla, pp351–359).

Isolation of rice photoperiod sensitivity genes enables the introduction of such genes into arbitrary cultivars by transformation methods to modify the photoperiod sensitivity in these cultivar lines, which ultimately permits regulation of the heading date of the rice. Therefore, breeding using such genes is a particularly efficient yet simple and reliable method as compared to conventional methods.

However, the isolation of genes involved in the photoperiod sensitivity of rice has not yet been reported.

DISCLOSURE OF THE INVENTION

This need in the art led to the present invention, and the object of the present invention is to provide novel plant photoperiod sensitivity genes, specifically genes derived from rice. Another object of the present invention is to modify plant photoperiod sensitivity using such genes to modify the flowering time of the plant. Furthermore, another object of the present invention is to provide methods for assessing plant photoperiod sensitivity.

The present inventors focused specifically on rice, for which a simple method to modify the heading date was desired, and vigorously carried out studies to isolate genes related to rice photoperiod sensitivity.

A quantitative trait locus of rice, Hd6, identified using a progeny derived from a cross between Nipponbare and Kasalath, is known to exist on chromosome 3. Additionally, according to analyses on the Hd6 region with a genetic background of Nipponbare using nearly isogenic lines (Yamamoto et al. (1996) Abstract for Plant Genome IV. p124), the Hd6 gene locus has been revealed to be the locus of photoperiod sensitivity genes.

The present inventors first aligned the Hd6 gene region by linkage analysis using yeast artificial chromosome (YAC) clones to isolate the photoperiod sensitivity gene Hd6, a gene whose existence was known but which had not yet been isolated.

Specifically, the present inventors conducted linkage analysis of a large segregating population (200+980=1180 plants), which analysis is essential for the isolation of the Hd6 gene. A CAPS marker was used in the analysis to improve the efficiency of performance. Furthermore, a fine-scale physical map of the YAC clones around the candidate region of the Hd6 gene was constructed based of the contig map of YAC clones constructed in the Rice Genome Research Program. The Hd6 gene region was delimited to a region between markers E11893 and Y3626L using DNA end-fragments of YAC clone and cDNA clones on respective YAC clones as RFLP markers.

Next, the present inventors aligned the Hd6 gene regions using P1 derived artificial chromosome (PAC) clones. More specifically, DNA clones around the Hd6 gene region determined by the above analysis were used to select, from the genomic library of Nipponbare, 7 PAC clones purportedly comprising the nucleotide sequence of the DNA clones. Further, the alignment state of these clones was investigated to reveal that the PAC clone P0689D1 contained the candidate region of the Hd6 gene (FIG. 1).

The present inventors successfully mapped the region wherein the Hd6 candidate gene was presumed to exist to a site of about 26.4 kb by analyzing the nucleotide sequence of the PAC clone P0689D1. Gene prediction analysis and similarity search was conducted against the nucleotide sequence of the candidate region to find a region showing high similarity with the Arabidopsis CKIIα gene (FIGS. 2 and 3). The CKIIα gene is reported to be involved in the activation of the CCA1 (circadian clock) gene in Arabidopsis.

The nucleotide sequence of the Kasalath genomic CKIIα gene was determined using the nucleotide sequence information of the Nipponbare CKIIα gene. Then, the two sequences were compared to each other. As a result, a termination codon was identified in the protein-coding region of the Nipponbare CKIIα gene, but not in that of Kasalath (FIGS. 4A–4H). The expression of the candidate gene CKIIα in Nipponbare, which is suggested to lack the photoperiod sensitivity gene Hd6, and in nearly isogenic lines of Nipponbare having the Hd6 gene of Kasalath was compared using the RT-PCR method to reveal that the transcription level of the Hd6 candidate gene, the CKIIα gene, is markedly low in Nipponbare as compared to Hd6 nearly isogenic lines (FIG. 7). From the above, the inventors concluded that the Kasalath CKIIα gene was the rice photoperiod sensitivity gene Hd6.

Thus, the use of the Hd6 gene and other plant genes having the same function as the Hd6 gene has been enabled by the isolation of the Hd6 gene, which confers photoperiod sensitivity to rice plants. The use of such genes allows for the modification of the heading date of rice, and further, for the modification of the flowering time in a wide variety of plants. Moreover, this allows for breeding plant cultivars with modified adaptability to cultivation locations and seasons.

Further, the present inventors revealed that a specific restriction enzyme Hind III recognition site in Kasalath is generated through a difference of a nucleotide between the ORF of Nipponbare Hd6 gene and that of Kasalath Hd6 gene. The use of the different nucleotide in determining the existence or absence of the photoperiod sensitivity genes in rice cultivars by a restriction enzyme fragment polymorphism analysis has been indicated. On the other hand, the photoperiod sensitivity gene E3 was proposed to exist on chromosome 3 and its position was proposed to correspond to the position of Hd6. Accordingly, the present inventors examined the validity of this restriction enzyme fragment polymorphism analysis on cultivar population, wherein the existence or absence of the photoperiod sensitivity gene E3 therein has been already determined by a genetic analysis (Okumoto et al. (1991) International Rice Research Institute, Rice Genetics II pp. 778–780). As a result, the inventors found that the amplified fragments of the Hd6 gene in cultivars determined to lack E3 were not digested with Hind III whereas those of 8 cultivars determined to retain E3 were digested with the enzyme. Thus, it was revealed by the present inventors that the photoperiod sensitivity of rice cultivars could be efficiently determined by methods identifying the existence or absence of a termination codon at a specific site in the Hd6 gene.

In other words, the present inventors succeeded in isolating a gene involved in photoperiod sensitivity of plants. The present inventors also found that the photoperiod sensitivity of plants can be modified using the gene, and that the photoperiod sensitivity of plants can be assessed by the gene, and finally completed the present invention.

More specifically, this invention provides the following:

(1) a DNA encoding a protein derived from plants that increases the photoperiod sensitivity of plants, said DNA being selected from the group of:

(a) a DNA encoding the protein comprising the amino acid sequence of SEQ ID NO: 1;

(b) a DNA encoding the protein comprising the amino acid sequence of SEQ ID NO: 1, wherein one or more of the amino acids are substituted, deleted, added and/or inserted;

(c) a DNA hybridizing under stringent conditions with the DNA consisting of the nucleotide sequence of SEQ ID NO: 2;

(2) the DNA of (1), wherein the DNA is derived from rice;

(3) a DNA encoding an antisense RNA complementary to the transcription product of the DNA of any one of (1) and (2);

(4) a DNA encoding an RNA having the activity of a ribozyme that specifically digests the transcription product of the DNA of (1) or (2);

(5) a DNA encoding an RNA that represses the expression of the DNA of (1) or (2) upon expression in a plant cell due to a corepressing effect;

(6) a DNA of (1) or (2), wherein the DNA is used to increase the photoperiod sensitivity of plants;

(7) a DNA of any one of (3) to (5), which DNA is used to reduce the photoperiod sensitivity of plants;

(8) a vector comprising the DNA of any one of (1) to (5);

(9) a plant cell transformed with the vector of (8);

(10) a plant transformant comprising the plant cell of (9);

(11) the plant transformant of (10), wherein said plant transformant is rice;

(12) a plant transformant which is a progeny or a clone of the plant transformant of (10) or (11);

(13) a breeding material of the plant transformant of any one of (10) to (12);

(14) a method for producing the plant transformant of (10) or (11), which comprises the following steps of:

(a) introducing the DNA of (1) or (2) into a plant cell, and (b) regenerating a plant from the plant cell;

(15) a method for increasing the photoperiod sensitivity of plants, said method comprising the step of expressing the DNA of (1) or (2) in cells of the plant body;

(16) the method of (15), wherein the flowering time of a plant dependent on the photoperiod is delayed by increasing the photoperiod sensitivity of the plant;

(17) a method for decreasing the photoperiod sensitivity of plants, said method comprising the step of repressing the expression of the DNA of (1) or (2) in cells of the plant body, wherein said DNA is endogenous to said plant cells;

(18) the method of (17), wherein the DNA of any one of (3) to (5) is expressed within the cells of the plant body;

(19) the method of (17) or (18), wherein the flowering of the plant dependent on the photoperiod is accelerated by the decrease in photoperiod sensitivity of the plant;

(20) a method of any one of (15) to (19), wherein the plant is rice;

(21) a method for assessing the photoperiod sensitivity of plants, comprising the step of detecting the presence or absence of the DNA of (1) in the plant;

(22) the method of (21), wherein the plant is rice;

(23) the method of (22), wherein substitution of the 2815th nucleotide, “A”, in the nucleotide sequence of SEQ ID NO: 2 for the nucleotide “T” is detected;

(24) the method of (23), further comprising the steps of:

(a) conducting polymerase chain reaction using rice genomic DNA as the template and primer pairs against the DNA consisting of the nucleotide sequence of SEQ ID NO: 2 or the complementary strand thereof, wherein said primer pairs are designed to sandwich the 2815th nucleotide “An” of the nucleotide sequence of SEQ ID NO: 2; (b) reacting the restriction enzyme Hind III with the DNA fragments amplified by the polymerase chain reaction in step (a); and (c) detecting whether the DNA fragments are digested by the action of the restriction enzyme Hind III;

(25) a host cell wherein a vector comprising the DNA of (1) or (2) has been inserted;

(26) a protein encoded by the DNA of (1) or (2);

(27) a method for producing the protein of (26) comprising the following steps of:

(a) culturing a host cell of (25), and (b) recovering the recombinant protein from the host cell or the culture supernatant thereof;

(28) an antibody binding to the protein of (26); and

(29) a DNA comprising at least 15 nucleotides that are complementary to a DNA consisting of the nucleotide sequence of SEQ ID NO: 2 or to a complementary strand thereof.

The present invention provides DNAs encoding the Hd6 protein derived from rice. The nucleotide sequences of the genomic DNA and cDNA of the Kasalath Hd6 isolated by the present inventors are shown in SEQ ID NO: 2 and 3, respectively. The amino acid sequence of the protein encoded by these DNAs is shown in SEQ ID NO: 1. Additionally, the nucleotide sequence of the Nipponbare Hd6 genomic DNA is shown in SEQ ID NO: 5, and the amino acid sequence of the protein encoded by the DNA is shown in SEQ ID NO: 4.

The Hd6 is one of quantitative trait loci (QTL) detected by using progeny lines of a cross between Nipponbare and Kasalath, and it was known to exist on chromosome 3. Additionally, it was known that the Hd6 locus was a photoperiod sensitivity gene locus according to an experiment using a nearly isogenic line on Hd6 region with a genetic background of Nipponbare. This nearly isogenic line needed about 5 to 7 days more for heading from seeding (heading date) as compared to that of Nipponbare. In other words, Hd6 can intensify the photoperiod sensitivity to delay heading. The Hd6 gene has been known to be a gene involved in photoperiod sensitivity of plants and to exist somewhere within the vast region of chromosome 3. However, the Hd6 gene had not been identified nor isolated. After performing complicated examination steps, the present inventors finally identified the region where the gene exists, and succeeded for the first time in isolating the gene as a single gene.

Today, it is an important object to control the heading date of rice in the breeding of rice in Japan. It is important to evade cold weather damage in cold districts due to the early coming of low-temperature of fall. On the other hand, to abridge the labor due to centralization of harvest time in the extensive rice-growing region in the west-south warm area, there is a need to accelerate or to delay the heading date.

The heading date of plants (flowering time) can be delayed by transforming plants with a DNA encoding the Hd6 protein which enhances the photoperiod sensitivity of plants. Alternatively, control of the expression of the DNA using the antisense method or the ribozyme method enables reduced photoperiod sensitivity, and accelerated flowering time of plants. Specifically, the flowering time of plants can be diversified by recombinantly introducing a DNA encoding the Hd6 protein to plants lacking the DNA and by controlling expression of the DNA in cultivars having the DNA using antisense, ribozymes, and such. Thus, new kinds of cultivars can be bred.

DNA encoding the Hd6 protein of the present invention includes genomic DNA, cDNA, and chemically synthesized DNA. A genomic DNA and cDNA can be prepared according to conventional methods known to those skilled in the art. More specifically, a genomic DNA can be prepared, for example, as follows: (1) extract genomic DNA from rice cultivars having the photoperiod sensitivity gene (e.g. Kasalath); (2) construct a genomic library (utilizing a vector, such as plasmid, phage, cosmid, BAC, and so on); (3) spread the library; and (4) conduct colony hybridization or plaque hybridization using a probe prepared based on the DNA encoding a protein of the present invention (e.g. SEQ ID NO: 2). Alternatively, a genomic DNA can be prepared by PCR, using primers specific to a DNA encoding the protein of s present invention (e.g. SEQ ID NO: 2). On the other hand, cDNA can be prepared, for example, as follows: (1) synthesize cDNAs based on mRNAs extracted from rice cultivars having the photoperiod sensitivity gene (e.g. Kasalath); (2) prepare a cDNA library by inserting the synthesized cDNA into vectors, such as λZAP; (3) spread the cDNA library; and (4) conduct colony hybridization or plaque hybridization as described above. Alternatively, cDNA can be also prepared by PCR.

The present invention includes DNAs encoding proteins functionally equivalent to the Hd6 protein of SEQ ID NO: 1. Herein, the term “functionally equivalent to the Hd6 protein” indicates that the object protein has the function of enhancing the photoperiod sensitivity of plants. Examples of such DNAs include those encoding mutants, derivatives, alleles, variants, and homologues comprising the amino acid sequence of SEQ ID NO: 1 wherein one or more amino acids are substituted, deleted, added and/or inserted.

Examples of methods for preparing a DNA encoding a protein comprising altered amino acids well known to those skilled in the art include the site-directed mutagenesis (Kramer, W. and Fritz, H.-J., “Oligonucleotide-directed construction of mutagenesis via gapped duplex DNA.” Methods in Enzymology, 154: 350–367, 1987). The amino acid sequence of a protein may also be mutated in nature due to the mutation of a nucleotide sequence. A DNA encoding proteins having the amino acid sequence of a natural Hd6 protein wherein one or more amino acids are substituted, deleted, and/or added are also included in the DNA of the present invention, so long as they encode a protein functionally equivalent to the natural Hd6 protein (SEQ ID NO: 1). Additionally, nucleotide sequence mutants that do not give rise to amino acid sequence changes in the protein (degeneracy mutants) are also included in the DNA of the present invention.

Assessment of whether a DNA encodes a protein that enhances the photoperiod sensitivity of plants or not can be performed as follows: The most general method involves transforming with the DNA a plant and growing the plant in a growth cabinet wherein the length of day can be changed. More specifically, plants are grown under short-day condition (generally, 9 to 10 hours) or long-day condition (14 to 16 hours), and the number of days needed from seeding to flowering (when the plant is rice, from seeding to heading) is compared between plants grown under these different conditions. Plants that show no difference in the number of days-to-heading between the long-day and short-day conditions are determined to lack photoperiod sensitivity. Plants that show a difference in the number of days-to-heading between the two conditions are determined to have photoperiod sensitivity, and the difference is considered as the degree of photoperiod sensitivity of the plant. In those cases where a growth cabinet is not available, the assessment can be also performed by growing plants in fields and in greenhouses with natural day length. Specifically, plants are seeded every 20th day and are grown under natural day length under constant temperature to determine days needed for flowering in respective plants. Generally, the heading of rice cultivars with strong photoperiod sensitivity are accelerated when seeded during August to February, and those seeded between April to July are delayed. On the other hand, days-to-heading in rice cultivars having weak photoperiod sensitivity is not influenced by the season of seeding and doesn't change greatly according to day length.

A DNA encoding a protein functionally equivalent to the Hd6 protein described in SEQ ID NO: 1 can be produced, for example, by methods well known to those skilled in the art including: methods using hybridization techniques (Southern, E.M.: Journal of Molecular Biology, Vol. 98, 503, 1975.); and polymerase chain reaction (PCR) techniques (Saiki, R. K. et al. Science, vol. 230, 1350–1354, 1985; Saiki, R. K. et al. Science, vol. 239, 487–491, 1988). That is, it is routine for a person skilled in the art to isolate a DNA with high homology to the Hd6 gene from rice and other plants using the nucleotide sequence of the Hd6 gene (SEQ ID NO: 2 or 3) or parts thereof as a probe, and oligonucleotides hybridizing specifically to the nucleotide sequence of Hd6 gene (SEQ ID NO: 2 or 3) as a primer. Such DNA encoding proteins functionally equivalent to the Hd6 protein, obtainable by hybridization techniques or PCR techniques, are included in the DNA of this invention.

Hybridization reactions to isolate such DNAs are preferably conducted under stringent conditions. Stringent hybridization conditions of the present invention include conditions such as: 6M urea, 0.4% SDS, and 0.5×SSC; and those which yield a similar stringency with the conditions. DNAs with higher homology are expected when hybridization is performed under conditions with higher stringency, for example, 6M urea, 0.4% SDS, and 0.1×SSC. Those DNAs isolated under such conditions are expected to encode a protein having a high amino acid level homology with Hd6 protein (SEQ ID NO: 1). Herein, high homology means an identity of at least 50% or more, more preferably. 70% or more, and much more preferably 90% or more (e.g. 95% or more). The degree of homology of one amino acid sequence or nucleotide sequence to another can be determined by following the algorithm BLAST by Karlin and Altschl (Proc. Natl. Acad. Sci. USA, 90: 5873–5877, 1993). Programs such as BLASTN and BLASTX were developed based on this algorithm (Altschul et al. J. Mol. Biol. 215: 403–410, 1990). To analyze a nucleotide sequences according to BLASTN based on BLAST, the parameters are set, for example, as score=100 and word length=12. On the other hand, parameters used for the analysis of amino acid sequences by the BLASTX based on BLAST include, for example, score=50 and word length=3. Default parameters of each program are used when using BLAST and Gapped BLAST program. Specific techniques for such analysis are known in the art (http://www.ncbi.nlm.nih.gov.)

The DNA of the present invention can be used, for example, to prepare recombinant proteins, produce plant transformants with altered photoperiod sensitivity, and so on.

A recombinant protein is usually prepared by inserting a DNA encoding a protein of the present invention into an appropriate expression vector, introducing said vector into an appropriate cell, culturing the transformed cells, and purifying expressed proteins. A recombinant protein can be expressed as a fusion protein with other proteins so as to be easily purified, for example, as a fusion protein with maltose binding protein in Escherichia coli (New England Biolabs, USA, vector pMAL series), as a fusion protein with glutathione-S-transferase (GST) (Amersham Pharmacia Biotech, vector pGEX series), or tagged with histidine (Novagen, pET series). The host cell is not limited so long as the cell is suitable for expressing the recombinant protein. It is possible to utilize yeasts or various animal, plant, or insect cells besides the above described E. coli. A vector can be introduced into a host cell by a variety of methods known to one skilled in the art. For example, a transformation method using calcium ions (Mandel, M. and Higa, A., J. Mol. Biol. 53: 158–162, (1970); Hanahan, D., J. Mol. Biol. 166: 557–580, (1983)) can be used to introduce a vector into E. coli. A recombinant protein expressed in host cells can be purified and recovered from the host cells or the culture supernatant thereof by known methods. When a recombinant protein is expressed as a fusion protein with maltose binding protein or other partners, the recombinant protein can be easily purified by affinity chromatography.

The resulting protein can be used to prepare an antibody that binds to the protein. For example, a polyclonal antibody can be prepared by immunizing immune animals, such as rabbits, with a purified protein of the present invention or its portion, collecting blood after a certain period, and removing clots. A monoclonal antibody can be prepared by fusing myeloma cells with the antibody-forming cells of animals immunized with the above protein or its portion, isolating a monoclonal cell expressing a desired antibody (hybridoma), and recovering the antibody from the said cell. The obtained antibody can be utilized to purify or detect a protein of the present invention. Accordingly, the present invention includes antibodies that binds to proteins of the invention.

A plant transformant with increased photoperiod sensitivity can be created using DNAs of the present invention. More specifically, a DNA encoding a protein of the present invention is inserted into an appropriate vector; the vector is introduced into a plant cell; and then, the resulting transformed plant cell is regenerated. The photoperiod sensitivity gene Hd6, isolated by the present inventors, functions to enhance the photoperiod sensitivity of rice, and can delay the heading date of rice. Therefore, the heading date of arbitrary cultivars can be controlled by transforming the cultivars with the gene and expressing the same. The time needed for transformation is remarkably short as compared to ordinary gene transfer by crossing. Furthermore, the fact that the transformation doesn't accompany other characteristical changes is also beneficial. Genes controlling the heading date of rice are newly identified and isolated herein, and controlling of heading date of rice is enabled for the first time by the present invention.

On the other hand, a plant transformant with reduced photoperiod sensitivity can be created using DNA that represses the expression of a DNA encoding a protein of the present invention: wherein the DNA is inserted into an appropriate vector, the vector is introduced into a plant cell, and then, the resulting transformed plant cell is regenerated. The phrase “repression of expression of DNA encoding a protein of the present invention” includes repression of gene transcription as well as repression of translation into protein. It also includes not only the complete inability of expression of DNA but also reduction of expression.

The expression of a specific endogenous gene in plants can be repressed by methods utilizing antisense technology, which are commonly used in the art. Ecker et al. were the first to demonstrate the antisense effect of an antisense RNA introduced by electroporation in plant cells by using the transient gene expression method (J. R. Ecker and R. W. Davis, Proc. Natl. Acad. Sci. USA 83: 5372 (1986)). Thereafter, the target gene expression was reportedly reduced in tobacco and petunias by expressing antisense RNAs (A. R. van der Krol et al., Nature 333: 866 (1988)). The antisense technique has now been established as a means to repress target gene expression in plants. Multiple factors are required for antisense nucleic acid to repress the target gene expression. These include: inhibition of transcription initiation by triple strand formation; repression of transcription by hybrid formation at the site where the RNA polymerase has formed a local open loop structure; transcription inhibition by hybrid formation with the RNA being synthesized; repression of splicing by hybrid formation at the junction between an intron and an exon; repression of splicing by hybrid formation at the site of spliceosome formation; repression of mRNA translocation from the nucleus to the cytoplasm by hybrid formation with mRNA; repression of splicing by hybrid formation at the capping site or at the poly A addition site; repression of translation initiation by hybrid formation at the binding site for the translation initiation factors; repression of translation by hybrid formation at the site for ribosome binding near the initiation codon; inhibition of peptide chain elongation by hybrid formation in the translated region or at the polysome binding sites of mRNA; and repression of gene expression by hybrid formation at the sites of interaction between nucleic acids and proteins. These factors repress the target gene expression by inhibiting the process of transcription, splicing, or translation (Hirashima and Inoue, “Shin Seikagaku Jikken Koza (New Biochemistry Experimentation Lectures) 2, Kakusan (Nucleic Acids) IV, Idenshi No Fukusei To Hatsugen (Replication and Expression of Genes)”, Nihon Seikagakukai Hen (The Japanese Biochemical Society), Tokyo Kagaku Dozin, pp. 319–347, (1993)).

An antisense sequence of the present invention can repress the target gene expression by any of the above mechanisms. In one embodiment, if an antisense sequence is designed to be complementary to the untranslated region near the 5‘end of the gene’s mRNA, it will effectively inhibit translation of a gene. It is also possible to use sequences complementary to the coding regions or to the untranslated region on the 3′ side. Thus, the antisense DNA used in the present invention include DNA having antisense sequences against both the untranslated regions and the translated regions of the gene. The antisense DNA to be used is connected downstream from an appropriate promoter, and, preferably, a sequence containing the transcription termination signal is connected on the 3′ side. The DNA thus prepared can be transfected into the desired plant by known methods. The sequence of the antisense DNA is preferably a sequence complementary to the endogenous gene of the plant to be transformed or a part thereof, but it need not be perfectly complementary so long as it can effectively inhibit the gene expression. The transcribed RNA is preferably at least 90%, and most preferably at least 95% complementary to the transcribed products of the target gene. In order to effectively inhibit the expression of the target gene by means of an antisense sequence, the antisense DNA should be at least 15 nucleotides long, more preferably at least 100 nucleotides long, and still more preferably at least 500 nucleotides long. The antisense DNA to be used is generally shorter than 5 kb, and preferably shorter than 2.5 kb.

DNA encoding ribozymes can also be used to repress the expression of endogenous genes. A ribozyme is an RNA molecule that has catalytic activities. There are many ribozymes having various activities. Research on the ribozymes as RNA cleaving enzymes has enabled the design of a ribozyme that site-specifically cleaves RNA. While some ribozymes of the group I intron type or the M1RNA contained in RNaseP consist of 400 nucleotides or more, others belonging to the hammerhead type or the hairpin type have an activity domain of about 40 nucleotides (Makoto Koizumi and Eiko Ohtsuka, Tanpakushitsu Kakusan Kohso (Nucleic acid, Protein, and Enzyme), 35: 2191 (1990)).

The self-cleavage domain of a hammerhead type ribozyme cleaves at the 3′ side of C15 of the sequence G13U14C15. Formation of a nucleotide pair between U14 and A at the ninth position is considered important for the ribozyme activity. Furthermore, it has been shown that the cleavage also occurs when the nucleotide at the 15th position is A or U instead of C (M. Koizumi et al., FEBS Lett. 228: 225 (1988)). If the substrate binding site of the ribozyme is designed to be complementary to the RNA sequences adjacent to the target site, one can create a restriction-enzyme-like RNA cleaving ribozyme which recognizes the sequence UC, UU, or UA within the target RNA (M. Koizumi et al., FEBS Lett. 239: 285 (1988); Makoto Koizumi and Eiko Ohtsuka, Tanpakushitsu Kakusan Kohso (Protein, Nucleic acid, and Enzyme), 35: 2191 (1990); M. Koizumi et al., Nucleic Acids Res. 17: 7059 (1989)). For example, in the coding region of the Hd6 gene (SEQ ID NO: 3), there are a plurality of sites that can be used as the ribozyme target.

The hairpin type ribozyme is also useful in the present invention. A hairpin type ribozyme can be found, for example, in the minus strand of the satellite RNA of tobacco ringspot virus (J. M. Buzayan, Nature 323: 349 (1986)). This ribozyme has also been shown to target-specifically cleave RNA (Y. Kikuchi and N. Sasaki, Nucleic Acids Res. 19: 6751 (1992); Yo Kikuchi, Kagaku To Seibutsu (Chemistry and Biology) 30: 112 (1992)).

The ribozyme designed to cleave the target is fused with a promoter, such as the cauliflower mosaic virus 35S promoter, and with a transcription termination sequence, so that it will be transcribed in plant cells. However, if extra sequences have been added to the 5′ end or the 3′ end of the transcribed RNA, the ribozyme activity can be lost. In this case, one can place an additional trimming ribozyme, which functions in cis to perform the trimming on the 5′ or the 3′ side of the ribozyme portion, in order to precisely cut the ribozyme portion from the transcribed RNA containing the ribozyme (K. Taira et al., Protein Eng. 3: 733 (1990); A. M. Dzaianott and J. J. Bujarski, Proc. Natl. Acad. Sci. USA 86: 4823 (1989); C. A. Grosshands and R. T. Cech, Nucleic Acids Res. 19: 3875 (1991); K. Taira et al. Nucleic Acid Res. 19: 5125 (1991)). Multiple sites within the target gene can be cleaved by arranging these structural units in tandem to achieve greater effects (N. Yuyama et al., Biochem. Biophys. Res. Commun. 186: 1271 (1992)). By using such ribozymes, it is possible to specifically cleave the transcription products of the target gene in the present invention, thereby repressing the expression of said gene.

Endogenous gene expression can also be repressed by co-repression through the transformation by DNA having a sequence identical or similar to the target gene sequence. “Co-repression” refers to the phenomenon in which, when a gene having a sequence identical or similar to the target endogenous gene sequence is introduced into plants by transformation, expression of both the introduced exogenous gene and the target endogenous gene becomes repressed. Although the detailed mechanism of co-repression is unknown, it is frequently observed in plants (Curr. Biol. 7: R793 (1997), Curr. Biol. 6: 810 (1996)). For example, if one wishes to obtain a plant body in which the Hd6 gene is co-repressed, the plant in question can be transformed with a vector DNA designed so as to express the Hd6 gene or DNA having a similar sequence to select a plant having the Hd6 mutant character, i.e., a plant with reduced photoperiod sensitivity, among the resultant plants. The gene to be used for co-repression does not need to be completely identical to the target gene, but it should have at least 70% or more sequence identity, preferably 80% or more sequence identity, and more preferably 90% or more (e.g. 95% or more) sequence identity. Sequence identity may be determined by above-described method.

In addition, endogenous gene expression in the present invention can also be repressed by transforming the plant with a gene having the dominant negative phenotype of the target gene. A gene having the dominant negative phenotype means a gene which, when expressed, can eliminate or reduce the activity of the wild type endogenous gene inherent to the plant.

Vectors used for the transformation of plant cells are not limited so long as the vector can express inserted genes in plant cells. For example, vectors comprising promoters for constitutive gene expression in plant cells (e.g., califlower mosaic virus 35S promoter); and promoters inducible by exogenous stimuli can be used. The term “plant cell” used herein includes various forms of plant cells, such as cultured cell suspensions, protoplasts, leaf sections, and callus.

A vector can be introduced into plant cells by known methods, such as the polyethylene glycol method, electroporation, Agrobacterium mediated transfer, and particle bombardment. Plants can be regenerated from transformed plant cells by known methods depending on the type of the plant cell (Toki et al., (1995) Plant Physiol. 100: 1503–1507). For example, transformation and regeneration methods for rice plants include: (1) introducing genes into protoplasts using polyethylene glycol, and regenerating the plant body (suitable for indica rice cultivars) (Datta, S. K. (1995) in “Gene Transfer To Plants”, Potrykus I and Spangenberg Eds., pp66–74); (2) introducing genes into protoplasts using electric pulse, and regenerating the plant body (suitable for japonica rice cultivars) (Toki et al (1992) Plant Physiol. 100, 1503–1507); (3) introducing genes directly into cells by the particle bombardment, and regenerating the plant body (Christou et al. (1991) Bio/Technology, 9: 957–962); (4) introducing genes using Agrobacterium, and regenerating the plant body (Hiei et al. (1994) Plant J. 6: 271–282); and so on. These methods are already established in the art and are widely used in the technical field of the present invention. Such methods can be suitably used for the present invention.

Once a transformed plant, wherein the DNA of the present invention is introduced into the genome, is obtained, it is possible to gain descendants from that plant body by sexual or vegetative propagation. Alternatively, plants can be mass-produced from breeding materials (for example, seeds, fruits, ears, tubers, tubercles, tubs, callus, protoplast, etc.) obtained from the plant, as well as descendants or clones thereof. Plant cells transformed with the DNA of the present invention, plant bodies including these cells, descendants and clones of the plant, as well as breeding materials obtained from the plant, its descendant and clones, are all included in the present invention.

The flowering time in plants with modified photoperiod sensitivity, prepared as above, is different from that of wild-type plants. For example, plants transformed with a DNA encoding the Hd6 protein have increased photoperiod sensitivity, and flowering time of the plant is delayed. On the other hand, plants wherein the expression of the DNA encoding the Hd6 protein is repressed due to the introduction of antisense DNAs, have reduced photoperiod sensitivity and the day-to-flowering of the plant is decreased. Thus, the time needed for flowering of plants can be regulated by controlling the expression of the Hd6 gene. According to the present invention, the heading date of rice, a valuable crop, can be closely controlled, which is extremely beneficial in the breeding of rice cultivars adapted to a particular environment.

Moreover, the present invention provides methods for assessing plant photoperiod sensitivity. According to the comparison of the Hd6 gene ORF of Kasalath, a functional allele of Hd6, and that of Nipponbare, a non-functional allele of Hd6, it was found out that only a nucleotide was substituted among the ORFs of these cultivars. The site encoding lysine in Kasalath is changed to a stop codon in the Hd6 gene ORF of Nipponbare by the substitution of a nucleotide. The stop codon in the Nipponbare gene prohibits translation of a functional product from the gene. This fact indicates that the expression of functional Hd6 proteins in a plant is one of the factors that determine the degree of photoperiod sensitivity of the plant. The method of assessing the photoperiod sensitivity of plants of the present invention is based on this finding and is characterized by the step of detecting whether a plant retains a DNA encoding a functional Hd6 protein.

The assessment of the photoperiod sensitivity of a plant based on whether the plant retains the DNA encoding a functional Hd6 protein or not can be performed on rice by detecting the mutation of the 2815th nucleotide “A” in the nucleotide sequence of SEQ ID NO: 2. Further, the restriction enzyme Hind III recognition site of the Kasalath Hd6 DNA is altered in that of Nipponbare so that the latter site cannot be recognized by the restriction enzyme Hind III, due to a difference in the nucleotide sequence of the Kasalath and Nipponbare Hd6 gene ORFs. The Hind III recognition site can be specifically detected in rice cultivars characterized as photoperiod sensitive cultivars by the existence of the photoperiod sensitivity E3 gene. Thus, the mutation of the nucleotide above can be detected by the presence or absence of recognition according to the restriction enzyme Hind III (CAPS (Cleaved Amplified Polymorphic Sequence) method). More specifically, the method using Hind III comprises the steps of: (a) conducting polymerase chain reaction using rice genome DNA as the template and primer pairs against the DNA consisting of the nucleotide sequence described in SEQ ID NO: 2 or a complementary strand thereof, which primer pairs are designed so as to contain, between them, the 2815th nucleotide “A” of the nucleotide sequence of SEQ ID NO: 2; (b) reacting the restriction enzyme Hind III with the DNA fragment amplified by the polymerase chain reaction in step (a); and (c) detecting whether the DNA fragments are digested by the restriction enzyme Hind III. Primers described in SEQ ID NO: 20 and 21 are examples of primer pairs that may be used in the above method. Whether the PCR product is digested by the action of the restriction enzyme Hind III or not can be determined by electrophoresis of the DNA fragments after treating them with the restriction enzyme, and detecting the pattern of electrophoresis. Subject plants whose PCR products are not digested with Hind III are determined to not possess a functional allele of Hd6.

In addition to the CAPS (Cleaved Amplified Polymorphic Sequence) method described above, the dCAPS method (Neff et al., The Plant Journal 14: 387–392, 1998) can be also used in the method of the present invention. The dCAPS method may be used in case where the site of nucleotide substitution does not correspond to the specific restriction enzyme recognition site. Specifically, primers are designed so that they hybridize to a sequence near the nucleotide substitution site, and a mismatch is introduced to a part of the primer so that a product amplified with the primer contains a new recognition site for a restriction enzyme. In fact, the present inventors used the primer “SEQ ID NO: 22/5′-CTTTGTGGAGGTCCAAACATTGTC-3′” as the primer including the mismatch, and primer “SEQ ID NO: 21/5′-CTACAGATCCACAGAACAGG-3′” as the primer common with that for the CAPS marker.

Additionally, the ASPCR (allele-specific PCR) method (Dan et al. Proc. Natl. Acad. Sci. USA 86: 2757–2760, 1989), wherein the primers are designed so that the 3′ end of one of the primers corresponds to the nucleotide substitution site and no amplification product can be obtained for one of the cultivars, can be also used in the present invention.

The assessment of the photoperiod sensitivity of plants using the method of the present invention is effective, for example, in breeding plants by crossing. That is, when the introduction of photoperiod sensitive character is undesirable, crossing with plants having photoperiod sensitivity can be avoided by the present invention. On the contrary, when the introduction of a photoperiod sensitive character is desired, crossing with cultivars having photoperiod sensitivity is enabled by the present invention. Furthermore, the present method is also useful in selecting plants from crossed progeny plants. Determination of the photoperiod sensitivity of plants at the gene sequence is simple and reliable as compared to a determination based on the phenotype of the plant. Thus, the method for assessment of the photoperiod sensitivity of the present invention contributes markedly to progress in breeding methods for plants.

Further, the present invention provides DNAs comprising at least 15 nucleotides that are complementary to a DNA of the present invention consisting of the nucleotide sequence of SEQ ID NO: 2 or to the complementary strand thereof. Herein, the term “complementary strand” is defined as one strand of a double stranded DNA composed of A:T and G:C base pairs to the other strand. In addition, “complementary” is defined as not only those completely matching within a region of at least 15 continuous nucleotides, but also having a homology of at least 70%, preferably at least 80%, more preferably 90%, and even more preferably 95% or higher within that region. Such DNAs are useful as probes to detect or isolate a DNA of the present invention, or as primers to amplify a DNA of the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 schematically shows a linkage map around the Hd6 region, and a physical map aligning YAC and PAC.

FIG. 2 schematically shows the presumed genes on the candidate genomic locus.

FIG. 3 schematically shows a fine-scale genetic map around the Hd6 region.

FIGS. 4A–4H compares the nucleotide sequence of the candidate gene CKIIα of Nipponbare (SEQ ID NO: 5) with that of Kasalath (SEQ ID NO: 2).

FIG. 5 shows alignment of the predicated amino acid sequences of the CKIIα genes from rice maize, Arabidopsis, human, fly, and nematode (SEQ ID NOS: 23–28).

FIG. 6 schematically shows the presumed gene on the candidate genomic locus.

FIG. 7 is an electrophoretogram showing the expression pattern of the candidate gene CKIIα analyzed by RT-PCR. “M” indicates the marker (λ/Hind III+φX174/Hae III). Templates used for respective lanes were as follows: lane 1, 6, and 11, total DNA of Nipponbare; lane 2, 7, and 12, total DNA of Hd6 NIL; lane 3, 8, and 13, total RNA of Nipponbare; lane 4, 5, 9, 10, 14, and 15, total RNA of Hd6 NIL. PCR primers used for the amplification in lane 1 to 5 were for actin gene amplification; those in lane 6 to 10 for C10214 (CKIIα on the same locus as Hd6) amplification; and those for lane 11 to 15 for R2856 (CKIIα on a different locus to Hd6) amplification.

FIG. 8 is an electrophoretogram showing the polymorphism between the genomic DNA of Nipponbare and that of Kasalath detected by the CAPS method.

BEST MODE FOR CARRYING OUT THE INVENTION

The present invention is illustrated in detail below with reference to following examples but is not to be construed as being limited thereto.

EXAMPLE 1 Alignment of the Hd6 Gene Region by Linkage Analysis and Yeast Artificial Chromosome (YAC) Clones

Advanced backcross progeny populations (1180 plants) of Nipponbare and Kasalath were grown on fields, and plants in which recombination had occurred near the Hd6 locus were selected as plants to isolate the Hd6 region. CAPS markers were used for efficient selection (Konieczny and Ausubel, Plant J. 4: 403–410 (1993)).

First, CAPS markers flanking the Hd6 gene region were constructed from RFLP markers, R2404 and C1329. The resulting products show polymorphism when R2404 is amplified by PCR using primers, “SEQ ID NO: 6/5′-GCAAAATGCCACTTTGTGGC-3′” and “SEQ ID NO: 7/5′-AACTTACGCTCAAATCAAAA-3′ (antisense)”, specific to the cDNA clone R2404, under the condition of: 94° C. for 2 minutes; 40 cycles of “94° C., 30 seconds; 58° C., 30 seconds; and 72° C., 1 minute”; and 72° C. for 7 minutes. On the other hand, polymorphism of C1329 is detected by conducting PCR using primers specific to C1329, “SEQ ID NO: 8/5′-TGTTGCCCTCATTATCTGCT-3′” and “SEQ ID NO: 9/5′-GGAGGTCGGAGTAAAGGAAA-3′ (antisense)” under the condition of: 94° C. for 2 minutes; 35 cycles of “94° C., 1 minute; 60° C., 2 minutes; and 72° C., 3 minutes”; and 72° C. for 7 minutes, and then, digesting with a restriction enzyme Eco T22I. Template DNAs used for PCR were extracted according to a modified method of Manner and Tenning (Plant Mol. Biol. Reptr. 15: 38–45 (1997)). More specifically, 2 to 3 cm long pieces of leaves were crushed in extraction buffer (100 mM Trsi-HCl (pH 8.0), 50 mM Na-EDTA, 1.25% SDS, 0.38% sodium bisulfate, 200 μg/ml proteinase K); the solution was centrifuged after incubation at 65° C. for 2 hours. The supernatant was treated with isopropanol, and then the precipitate was dried and dissolved in an appropriate amount of water. 40 plants in total were selected as recombinants, wherein recombination occurred between the CAPS marker R2404 and C1329.

DNA was extracted from selected plants, and RFLP markers near the Hd6 gene were used to construct a detailed linkage map. The genotype of the Hd6 gene locus was determined by a progeny test. More specifically, selfed progeny of selected plants were grown on fields and the genotype was determined from the distribution of the days-to-heading of respective plants of respective lines. The Hd6 gene was demonstrated to exist between the RFLP marker R2404 and G1015, and was determined to co-segregate with R2856.

Using the detailed linkage map, a detailed alignment map was constructed on the basis of information from an alignment map of YAC clones prepared in the Rice Genome Research. All markers used for the linkage map were confirmed to be contained in respective YAC clones by Southern hybridization and PCR using STS primers of respective markers. Additionally, DNA end-fragments of YAC clones existing on the Hd6 region and cDNA clones existing on respective YAC clones were similarly analyzed.

During the analysis, contrary to other markers, R2856 could be detected in YAC clones existing on the Hd6 region by Southern hybridization, but, according to the result of PCR, was identified as a marker not existing on that YAC. This result suggests that a region highly homologous to the R2856 marker and to which the R2856 marker hybridizes exists on the candidate region of Hd6 gene; however, a gene encoding the cDNA clone R2856 does not exist therein. That is, the R2856 is an RFLP marker that has an extremely high homology with the sequence in the Hd6 region, but is originally encoded by a gene existing on other regions of the genome.

PCR analysis was conducted using R2856 specific primers, “SEQ ID NO: 10/5′-AGCACTCAAAAACACCAAGC-3′” and “SEQ ID NO: 11/5′-AACAAAGATACAAACAGCAC-3′ (antisense)”, under the following condition: 94° C. for 2 minutes; 30 cycles of “94° C. for 1 minute, 60° C. for 2 minutes, and 72° C. for 3 minutes”; and 72° C. for 7 minutes.

C10214 (Ac. No. D22035) was identified as a clone having high homology with R2856 from EST clones of Nipponbare (DDBJ (DNA Data Bank of Japan), which clones were analyzed in the Rice Genome Research Program. PCR was conducted under the same condition as above with C10214 specific primers, “SEQ ID NO: 12/5′-CTTGATCCTCAGCTTGAAGCT-3′” and “SEQ ID NO: 13/5′-TGCAAGGCTACAAGCACATTC-3′ (antisense)”, to confirm the existence of a gene encoding C10214 on the Hd6 region. As a result, it was demonstrated that the gene encoded by the clone exists on the Hd6 region.

Further, a more detailed linkage map was constructed based on the detailed alignment map of YAC clones using respective YAC DNA end-fragments and cDNA clones on the YAC clone as the RFLP markers. The result demonstrated the Hd6 gene region to exist between the marker E11893 and Y3626L (FIG. 1).

Example 2 Alignment of Hd6 Gene Region Using P1 Derived Artificial Chromosome (PAC) Clones

STS primers were prepared from the nucleotide sequence of ESTs and YAC end-fragments near the Hd6, C10214, E11893, Y3626L, C63403, C11482, and C60478, to screen the Nipponbare PAC genomic clone library (8352 clones, average insert length 112 kb). Conversion into STS was conducted with primers SEQ ID NO: 12 and 13 (described above) for C10214; “SEQ ID NO: 14/5′-TCGTCGCGCTCATAGCTAGA-3′” and “SEQ ID NO: 15/5′-ACTTCCTCGCTATGCCACAG-3′(antisense)” for E11893; and “SEQ ID NO: 16/5′-GCCCATAATGATACGATATACT-3′” and “SEQ ID NO: 17/5′-TGGTGGTGGTTGCTGTTCGA-3′” for Y3626L. Primers for EST mapping generated by the Rice Genome Research Program were used for C63403, C11482, and C60478. The condition for PCR was: 94° C. for 2 minutes; 35 cycles of “94° C. for 30 seconds, 60° C. for 1 minute, and 72° C. for 1 minute”; and 72° C. for 7 minutes. As a result, 7 clones expected to include genomic fragments near the Hd6 were selected. Further, end-fragments of these clones were used as a probe for RFLP analysis to reveal that PAC clone P689D1 comprised all the candidate gene region of Hd6.

Example 3 Determination of the Candidate Gene Region by Nucleotide Sequence Analysis

Nucleotide sequence analysis of PAC clone P0689D1, which is expected to contain the Hd6 gene, was performed. To analyze the nucleotide sequence, insert DNA (including the vector) of P0689D1 was fragmented with ultrasonication to prepare a sublibrary with an average insert length of 2 kb to 5 kb. Nucleotide sequences of 2000 clones randomly selected thereof were analyzed and were assembled using the computer software Phred/Phrap. New CAPS markers were produced according to the nucleotide sequence information of the candidate gene region specified by linkage analysis to delimit the candidate region where the candidate gene exists to a region of about 47 kb. Gene prediction by the computer program GENSCAN and BLAST homology search of nucleotide sequence of the candidate region revealed a region with extremely high homology with the CKIIα gene of Arabidopsis. Additionally, the nucleotide sequence of the region was concordant with that of the EST clone C10214 (FIG. 2). The CKIIα gene of Arabidopsis is demonstrated to influence the expression of several genes which expression is regulated by light (Lee et al. Plant Physiol. 119: 989–1000 (1999)), and to activate the circadian clock gene CCA1 protein by phosphorylation (Sugano et al. Proc. Natl. Acad. Sci. USA 95: 11020–11025 (1998)).

Example 4 Fine-Scale Linkage Analysis

A large population was subjected to linkage analysis to more precisely determine the Hd6 gene candidate region. Plants having recombination between CAPS markers R2404 and G1015, markers that flank the Hd6 gene, were newly selected from a segregating population of 1627 plants according to the method described above. Polymorphism of the clones was analyzed by PCR using G1015 specific primers “SEQ ID NO: 18/5′-CTGCAAGTTCAAGCCGATCA-3′” and “SEQ ID NO: 19/5′-TTGCAATTGGCTAAGCAAGAC-3′”, under the condition: 40 cycles of “94° C. for 40 seconds, 65° C. for 40 seconds, and 72° C. for 90 seconds”, and 72° C. for 7 minutes; followed by digestion of the obtained amplification product by the restriction enzyme Hae III. 11 plants were newly selected as plants with recombination in the Hd6 candidate gene region (between E11893 and Y3626L). DNA was extracted from these plants, and a detailed genetic map was made using CAPS markers together with the 4 recombinant plants identified by the former linkage analysis. The CAPS markers were prepared based the nucleotide sequence analysis described below. The genotype of Hd6 gene locus was determined by the progeny test as described above. The result demonstrated the Hd6 gene to be located between the CAPS marker, cnt13GNheI and cnt13BBglII; and to cosegregate with cnt13CRsaI, cnt912HindIII, and A5M7AluI (FIG. 3). The candidate region of Hd6 gene was mapped on a genomic region of 26.4 kb.

Example 5 Comparison Between the CKIIα Gene Nucleotide Sequences of Kasalath and Nipponbare

The genomic nucleotide sequence of the CKIIα gene of Kasalath was determined using the nucleotide sequence information of the CKIIα gene of Nipponbare, which, in turn, was determined by analysis of the PAC clone. More specifically, primers enabling amplification of specific region of the candidate gene were prepared, fragments were amplified using Kasalath genomic DNA as the template, and were cloned to analyze the nucleotide sequence. Nucleotide sequence was analyzed by changing the primers so as to hybridize to a nearby sequence to determine the entire nucleotide sequence around the CKIIα gene. Comparison of the Kasalath and Nipponbare CKIIα genes revealed multiple substitution, deletion and insertion of nucleotides, but only one of the nucleotide substitutions was in the ORF. The substitution results in a stop codon in Nipponbare, whereas the site encodes a lysine in Kasalath (FIGS. 4A–4H; SEQ ID NO: 2). It is considered that the CKIIα gene encodes a functional protein of 333 amino acids in Kasalath, whereas it cannot be translated as a functional product in Nipponbare due to the existence of the stop codon.

Example 6 Expression Pattern Analysis of the Candidate Gene, CKIIα

The difference in the expression level of the candidate CKIIα gene in Nipponbare, which is supposed to lack the photoperiodic sensitivity gene Hd6, and near isogenic lines of Nipponbare, that has the Kasalath Hd6 gene, was analyzed by RT-PCR. The nucleotides described above as SEQ ID NO: 7 and 8 were used as primers. The condition for PCR was as follows: 94° C. for 2 minutes; 25 cycles of “94° C. for 30 seconds, 62° C. for 40 seconds, and 72° C. for 1 minute”; and 72° C. for 7 minutes. As a result, no difference in the expression level of actin gene and CKIIα gene existing in other region than Hd6 could be detected, whereas the expression level of the candidate CKIIα gene was markedly low in Nipponbare compared to Hd6 near isogenic lines (FIG. 7).

Example 7 Method for Evaluating Photoperiod Sensitivity in Rice Cultivars

Among the photoperiod sensitivity genes whose existence has been genetically demonstrated, the E3 gene has been suggested to exist on chromosome 3. Therefore, the relationship between E3 and Hd6 was demonstrated using a simple method for identifying differences in the nucleotide sequence of Hd6 coding region in Nipponbare and Kasalath. The mutated nucleotide site (substitution of the 2815th nucleotide from “A” to “T” in SEQ ID NO: 2) existing on the Hd6 gene of Nipponbare and Kasalath is within the recognition site of a restriction enzyme Hind III, and the inventors revealed that the Hd6 gene is digested in Kasalath but not in Nipponbare. Thus, a DNA fragment of 543 bp, including the mutated nucleotide site, was amplified with primers, “SEQ ID NO: 20/5′-ACCTGGCAGCATGTTATGAC-3′ (sense, first intron)” and “SEQ ID NO: 21/5′-CTACAGATCCACAGAACAGG-3′ (antisense, third intron)”. When the amplified DNA fragment has the Kasalath sequence (without a stop codon), the fragment is digested by the treatment with the restriction enzyme Hind III into two fragments with lengths of 329 bp and 214 bp; those with other sequences could not be digested (FIG. 8). Thus, it was indicated that the method could be used for identifying genes that confer photoperiod sensitivity to plants. Next, the efficiency of the method was tested using cultivars, wherein the existence or absence of the E3 gene has been already proven by genetic analysis (Okumoto et al. International Rice Research Institute, Rice Genetics II pp. 778–780 1991). The fragments amplified from the genes of 8 cultivars, which were demonstrated to lack the E3 gene, were not digested, whereas those of other 8 cultivars that were shown to have the E3 gene were digested (Table 1).

TABLE 1 Cultivar genotype CAPS analysis Kinmaze E3 + Koshihikari e3 − Manryo e3 − Nipponbare e3 − Nakateshinsenbon E3 + Hoyoku E3 + Akebono E3 + Norin 6 e3 − Fujiminori E3 + Fujisaka 5 E3 + Kiyonishiki e3 − Norin 1 e3 − Norin 8 e3 − Shiranui E3 + Norin 22 e3 − Zuiho E3 + Genotype E3: photoperiod sensitivity gene E3 Genotype e3: lacking photoperiod sensitivity gene E3 CAPS analysis +: including the Hind III recognition site, and is digested with Hind III. CAPS analysis −: lacking a Hind III recognition site, and isn't digested with Hind III.

Thus, the possibility that the Hd6 gene corresponds to the E3 gene is extremely high, and it is conceivable that the newly developed method to detect the stop codon of the present invention is an efficient tool to assess the photoperiod sensitivity of Hd6 or E3 genes.

Example 8 Production of Transgenic Plants Expressing the Hd6 Gene and Date-to-Heading Thereof

A genomic fragment (Nhe I-Bgl II 8.9 kb) comprising the CKIIα gene of Kasalath, which gene was considered to be the candidate gene of Hd6, was inserted into the binary vector pPZP2H-lac to produce a plasmid pPZPCKII-10A. Then, Nipponbare was transformed with the plasmid using Agrobacterium. No apparent difference could be detected in the transformed generation (T0), because the timing of shoot regeneration did not match between plants transformed with the vector alone and those transformed with pPZPCKII-10A. Thus, the selfed progeny of the two transformed plants as well as Nipponbare, near isogenic lines of Hd6 [NIL (Hd6)], and selfed progeny of the plant transformed with the vector alone were seeded in a closed growth chamber (Tsukuba, Ibaraki) on May 16 to investigate the heading date of respective plants. The number of plants whose first panicle had appeared where every two days (Table 2).

The heading dates of progenies of plants transformed with the candidate gene showed segregation, the plants of early heading had a transgene and the plants showing late heading did not have a transgene. The heading date of early and late heading plants were almost the same as those of Nipponbare and NIL (Hd6), respectively. The heading date of all progenies of plants transformed with the vector alone were the same as those of Nipponbare. These results strongly suggest that the candidate CKIIα gene has the function of the Hd6 gene to delay the heading date under natural field condition.

TABLE 2 heading date 93 95 97 99 101 103 105 107 109 111 113 115 117 Nipponbare 3  6 1  NIL (Hd6) 1 3 4 vector alone 3  6 2  pPZPCKII-10A 1* 1* 8 3 transformant 1 pPZPCKII-10A 1* 1 2 1 1 1 transformant 2 *indicates plants without pPZPCKII-10A

INDUSTRIAL APPLICABILITY

The present invention provides photoperiod sensitivity genes in rice cultivars. The genes of the present invention confer photoperiod sensitivity to rice plants and may be used to control the heading date of rice. Therefore, the genes may be very useful in breeding. The heading date of rice plants can be changed by the use of the genes of the invention. Thus, the genes are particularly useful for breeding rice cultivars adapted to particular locations and seasons to grow the plant. Furthermore, the method to breed rice cultivars using a gene of the present invention is beneficial as compared to conventional methods, in that an object plant can be obtained in a short period with high reliability.

Further, the present invention provides methods for assessing the photoperiod sensitivity of plants. Two to three years of exceeding labor was needed to determine the photoperiod sensitivity of one cultivar according to conventional assessment methods which consist of: crossing object cultivars with test plant lines to identify the existence of a specific gene; and then, determining the existence of the gene by the segregation of the heading date in the progeny of the plants. According to the present method, the photoperiod sensitivity of a plant can be determined by: only (1) harvesting a part of the seedling about 2 weeks after seeding; (2) extracting the DNA thereof; and (3) determining after PCR using the DNA as the template and restriction enzyme treatment. The degree of photoperiod sensitivity of progenies of plants can be determined prior to crossing, based on the presence or absence of the gene, which is a valuable information for selecting and screening parent plant to be crossed. Furthermore, the presence or absence of the photoperiod sensitivity gene in each selected plant can be easily determined using the methods as described above. Thus, the gene serves also as selection markers. 

1. An isolated DNA encoding the protein comprising the amino acid sequence of SEQ ID NO:
 1. 2. A vector comprising the DNA of claim
 1. 3. A plant cell transformed with the vector of claim
 2. 4. A plant transformant comprising the plant cell of claim
 3. 5. The plant transformant of claim 4, wherein said plant transformant is rice.
 6. A plant transformant which is a progeny plant or a clonal plant of the plant transformant of claim 4 and wherein the progeny plant or clonal plant comprises the vector of claim
 2. 7. A breeding material of the plant transformant of claim 4 comprising the DNA of claim
 1. 8. A method for producing a plant transformant, which comprises the following steps of: (a) introducing the DNA of claim 1 into a plant cell, and (b) regenerating a plant transformant from the plant cell.
 9. A method for increasing the photoperiod sensitivity of a plant, said method comprising introducing into said plant the DNA of claim
 1. 10. The method of claim 9, wherein flowering in said plant is delayed compared to a wild-type plant.
 11. The method of claim 9, wherein the plant is rice.
 12. An isolated host cell comprising a vector, said vector comprising the DNA of claim
 1. 